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FF:11594-120H1: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:11, 29 March 2012


Name:Renal Glomerular Endothelial Cells, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuekidney
dev stageNA
sexNA
ageNA
cell typeendothelial cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:sc1101
catalog numberSC4005
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.00395
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.0238
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12086

Jaspar motifP-value
MA0002.20.444
MA0003.10.283
MA0004.10.457
MA0006.10.198
MA0007.10.0228
MA0009.10.445
MA0014.10.781
MA0017.10.0997
MA0018.25.77821e-5
MA0019.10.0968
MA0024.10.376
MA0025.10.158
MA0027.10.694
MA0028.10.198
MA0029.10.389
MA0030.10.0407
MA0031.10.0132
MA0035.20.0031
MA0038.10.326
MA0039.20.325
MA0040.10.113
MA0041.10.145
MA0042.10.549
MA0043.14.76507e-9
MA0046.10.354
MA0047.20.33
MA0048.10.173
MA0050.10.192
MA0051.10.878
MA0052.10.981
MA0055.10.0324
MA0057.10.325
MA0058.10.274
MA0059.10.246
MA0060.10.0286
MA0061.10.737
MA0062.20.0366
MA0065.20.0524
MA0066.10.316
MA0067.10.113
MA0068.10.764
MA0069.10.106
MA0070.10.0816
MA0071.10.0225
MA0072.10.824
MA0073.10.58
MA0074.10.46
MA0076.10.00271
MA0077.10.00104
MA0078.10.0763
MA0079.20.368
MA0080.20.0119
MA0081.10.299
MA0083.10.612
MA0084.10.728
MA0087.10.988
MA0088.10.341
MA0090.10.453
MA0091.10.537
MA0092.10.902
MA0093.10.434
MA0099.28.22807e-8
MA0100.10.208
MA0101.10.546
MA0102.22.64129e-5
MA0103.10.789
MA0104.20.959
MA0105.10.607
MA0106.10.0039
MA0107.10.65
MA0108.20.776
MA0111.10.962
MA0112.20.176
MA0113.10.109
MA0114.10.331
MA0115.10.938
MA0116.10.439
MA0117.10.144
MA0119.10.0423
MA0122.10.179
MA0124.10.707
MA0125.10.809
MA0131.10.337
MA0135.10.435
MA0136.10.448
MA0137.20.112
MA0138.20.286
MA0139.10.178
MA0140.10.084
MA0141.14.63689e-4
MA0142.10.83
MA0143.10.991
MA0144.10.245
MA0145.10.127
MA0146.10.0952
MA0147.10.722
MA0148.10.0587
MA0149.10.0564
MA0150.10.146
MA0152.10.835
MA0153.10.363
MA0154.10.215
MA0155.10.0367
MA0156.10.433
MA0157.10.178
MA0159.10.08
MA0160.10.0667
MA0162.10.0457
MA0163.10.159
MA0164.10.576
MA0258.10.456
MA0259.10.679



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12086

Novel motifP-value
10.413
100.849
1000.497
1010.174
1020.577
1030.628
1040.994
1050.811
1060.226
1070.0438
1080.295
1090.092
110.0254
1100.0192
1110.275
1120.259
1130.829
1140.333
1150.564
1160.447
1170.52
1180.275
1190.31
120.319
1200.0215
1210.761
1220.994
1230.0704
1240.185
1250.833
1260.675
1270.984
1280.45
1290.0691
130.247
1300.991
1310.0956
1320.108
1330.498
1340.867
1350.0567
1360.101
1370.447
1380.992
1390.793
140.981
1400.3
1410.518
1420.908
1430.0872
1440.407
1450.291
1460.35
1470.163
1480.328
1490.036
150.676
1500.233
1510.661
1520.0631
1530.066
1540.321
1550.836
1560.194
1570.508
1580.453
1590.327
160.65
1600.00593
1610.701
1620.248
1630.701
1640.419
1650.369
1660.0765
1670.202
1680.343
1690.0334
170.112
180.853
190.161
20.351
200.611
210.663
220.097
230.23
240.708
250.72
260.168
270.114
280.254
290.502
30.567
300.826
310.911
320.866
330.348
340.0424
350.873
360.0768
370.166
380.237
390.284
40.927
400.00422
410.0456
420.668
430.417
440.281
450.274
460.162
470.228
480.0374
490.796
50.967
500.452
510.37
520.696
530.779
540.536
550.759
560.478
570.31
580.412
590.0236
60.458
600.785
610.562
620.859
630.261
640.161
650.103
660.526
670.373
680.0802
690.343
70.724
700.681
710.336
720.454
730.00962
740.478
750.157
760.434
770.0311
780.551
790.101
80.0159
800.764
810.596
820.609
830.949
840.112
850.371
860.95
870.096
880.757
890.157
90.311
900.191
910.38
920.441
930.292
940.832
950.0139
960.521
970.977
980.279
990.00786



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs12086


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000115 (endothelial cell)
0000213 (lining cell)
0000215 (barrier cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000666 (fenestrated cell)
0002078 (meso-epithelial cell)
0002188 (glomerular endothelial cell)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000025 (tube)
0000058 (duct)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000074 (renal glomerulus)
0000080 (mesonephros)
0000083 (mesonephric tubule)
0000119 (cell layer)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000489 (cavitated compound organ)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001008 (renal system)
0001062 (anatomical entity)
0001225 (cortex of kidney)
0001229 (renal corpuscle)
0001230 (glomerular capsule)
0001285 (nephron)
0001851 (cortex)
0002050 (embryonic structure)
0002100 (trunk)
0002113 (kidney)
0002120 (pronephros)
0002417 (abdominal segment of trunk)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003060 (pronephric duct)
0003064 (intermediate mesoderm)
0003074 (mesonephric duct)
0003081 (lateral plate mesoderm)
0003103 (compound organ)
0003104 (mesenchyme)
0003220 (metanephric mesenchyme)
0003886 (body cavity precursor)
0003887 (intraembryonic coelom)
0003914 (epithelial tube)
0003918 (kidney mesenchyme)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004198 (comma-shaped body)
0004199 (S-shaped body)
0004208 (nephrogenic mesenchyme)
0004209 (renal vesicle)
0004819 (kidney epithelium)
0004875 (nephrogenic cord)
0004876 (urogenital ridge)
0005095 (kidney rudiment)
0005103 (mesonephric epithelium)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005721 (pronephric mesoderm)
0005749 (glomerular tuft)
0005754 (rostral part of nephrogenic cord)
0006553 (renal duct)
0006554 (urinary system structure)
0006555 (excretory tube)
0007684 (uriniferous tubule)
0007687 (kidney field)
0009142 (entire embryonic mesenchyme)
0009201 (nephric duct)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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